<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:"Times New Roman \(Body CS\)";
panose-1:2 11 6 4 2 2 2 2 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
font-size:12.0pt;
font-family:"Calibri",sans-serif;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Arial",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:12.0pt;
font-family:"Calibri",sans-serif;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Hi, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">I am using phenix.ligandfit to automatically fit a ligand in to the ligand site of a protein model using the experimentally derived structure factors for the complex. The ligand
pdb and restraints are created using phenix.elbow which contains the hydrogen atoms. However, after phenix.ligandfit the coordinates that are derived is stripped of all the ligand hydrogens. I want to retain the hydrogens only on the ligand during the refinement
to preserve the overall geometry of the ligand. I am trying to do this automatically over several datasets with different ligands. I don’t see any specific parameter in the phenix.ligandfit that would specifically allow me to retain the ligand hydrogens. Phenix.reduce
or phenix.ready_set does add hydrogens to entire coordinates including protein residues and so could not use it directly.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Is there a way to get this accomplished in a simple way? <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Thanks in advance and appreciate your suggestions.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Rangarajan. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"></span><span style="font-family:"Arial",sans-serif"><o:p></o:p></span></p>
</div>
</body>
</html>